rs668998

Positions:

• chr3-159997764-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_108088.1(IL12A-AS1):​n.1084+80C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 151,982 control chromosomes in the GnomAD database, including 30,689 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.62 (30683 hom., cov: 31)
  • Exomes 𝑓: 0.75 (6 hom.)
• Consequence: IL12A-AS1 NR_108088.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.785

Genes affected

IL12A-AS1 (HGNC:49094): (IL12A antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL12A-AS1	NR_108088.1	n.1084+80C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL12A-AS1	ENST00000497452.5	n.1084+80C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94253 AN: 151848 Hom.: 30639 Cov.: 31

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.573

GnomAD4 exome AF: 0.750 AC: 12 AN: 16 Hom.: 6 AF XY: 0.667 AC XY: 8 AN XY: 12

Gnomad4 ASJ exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.667

GnomAD4 genome AF: 0.621 AC: 94359 AN: 151966 Hom.: 30683 Cov.: 31 AF XY: 0.613 AC XY: 45551 AN XY: 74276

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.575

Alfa AF: 0.568 Hom.: 41032

Bravo AF: 0.627

Asia WGS AF: 0.493 AC: 1714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.39
DANN	Benign	0.47

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs668998; hg19: chr3-159715551; COSMIC: COSV59759410;